From 614c72c65c00840020b72e5255c02ac33ee79e60 Mon Sep 17 00:00:00 2001
From: nkumar2 <nkumar2@ebi.ac.uk>
Date: Mon, 30 Sep 2024 09:33:06 +0100
Subject: [PATCH] minor updates

---
 pom.xml                                        |  5 +++++
 .../mongo/entity/subdocuments/HgvsMongo.java   |  4 ++++
 .../subdocuments/VariantSourceEntryMongo.java  | 18 ++++++++++++++++++
 .../entity/subdocuments/VariantStatsMongo.java | 13 +++++++++++++
 4 files changed, 40 insertions(+)

diff --git a/pom.xml b/pom.xml
index cd908cf83..de96bce84 100644
--- a/pom.xml
+++ b/pom.xml
@@ -8,6 +8,7 @@
     <artifactId>eva-pipeline</artifactId>
     <version>2.9.8-SNAPSHOT</version>
 
+    <packaging>jar</packaging>
 
     <parent>
         <groupId>org.springframework.boot</groupId>
@@ -177,9 +178,13 @@
                 <artifactId>spring-boot-maven-plugin</artifactId>
                 <executions>
                     <execution>
+                        <id>repackage</id>
                         <goals>
                             <goal>repackage</goal>
                         </goals>
+                        <configuration>
+                            <classifier>exec</classifier>
+                        </configuration>
                     </execution>
                 </executions>
             </plugin>
diff --git a/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/subdocuments/HgvsMongo.java b/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/subdocuments/HgvsMongo.java
index 2841fed5c..8757b2ddb 100644
--- a/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/subdocuments/HgvsMongo.java
+++ b/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/subdocuments/HgvsMongo.java
@@ -40,4 +40,8 @@ public HgvsMongo(String type, String name) {
         this.type = type;
         this.name = name;
     }
+
+    public String getName() {
+        return name;
+    }
 }
diff --git a/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/subdocuments/VariantSourceEntryMongo.java b/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/subdocuments/VariantSourceEntryMongo.java
index a75b653d3..30369a4b3 100644
--- a/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/subdocuments/VariantSourceEntryMongo.java
+++ b/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/subdocuments/VariantSourceEntryMongo.java
@@ -71,6 +71,20 @@ public class VariantSourceEntryMongo {
         // Spring empty constructor
     }
 
+    public VariantSourceEntryMongo(String fileId, String studyId, String[] alternates, BasicDBObject attrs, String format, BasicDBObject samp) {
+        this.fileId = fileId;
+        this.studyId = studyId;
+        if (alternates != null && alternates.length > 0) {
+            this.alternates = Arrays.stream(alternates)
+                    .map(a -> a.toUpperCase())
+                    .collect(Collectors.toList())
+                    .toArray(new String[0]);
+        }
+        this.attrs = attrs;
+        this.format = format;
+        this.samp = samp;
+    }
+
     public VariantSourceEntryMongo(String fileId, String studyId, String[] alternates, Map<String, String> attributes) {
         this.fileId = fileId;
         this.studyId = studyId;
@@ -193,4 +207,8 @@ public String[] getAlternates() {
     public BasicDBObject getAttrs() {
         return attrs;
     }
+
+    public String getFormat() {
+        return format;
+    }
 }
diff --git a/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/subdocuments/VariantStatsMongo.java b/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/subdocuments/VariantStatsMongo.java
index e66a3071b..c6cd9ca01 100644
--- a/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/subdocuments/VariantStatsMongo.java
+++ b/src/main/java/uk/ac/ebi/eva/commons/models/mongo/entity/subdocuments/VariantStatsMongo.java
@@ -81,6 +81,19 @@ public class VariantStatsMongo {
         //Empty constructor for spring
     }
 
+    public VariantStatsMongo(String studyId, String fileId, String cohortId, float maf, float mgf, String mafAllele, String mgfGenotype, int missingAlleles, int missingGenotypes, Map<String, Integer> numGt) {
+        this.studyId = studyId;
+        this.fileId = fileId;
+        this.cohortId = cohortId;
+        this.maf = maf;
+        this.mgf = mgf;
+        this.mafAllele = mafAllele;
+        this.mgfGenotype = mgfGenotype;
+        this.missingAlleles = missingAlleles;
+        this.missingGenotypes = missingGenotypes;
+        this.numGt = numGt;
+    }
+
     public VariantStatsMongo(String studyId, String fileId, String cohortId, VariantStats stats) {
         this.studyId = studyId;
         this.fileId = fileId;